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Submit High-throughput Sequencing Reads to NCBI Sequence Read Archive (SRA)

Goal

This workflow enables CyVerse users to make submissions to the NCBI Sequence Read Archive (SRA). A submission included compressed sequenced files (FASTQ.gz, SFF.gz, and BAM.gz) and an XML metadata file, organized into a package. If you need to submit an alternative file format (HD5, SOLiD, and SRF) please email support@cyverse.org


.. toctree::
        :maxdepth: 2

        Quickstart home <self>
        Create and organize an SRA submission package <step1.rst>
        Record metadata and associate with SRA submission <step2.rst>
        Validate and submit package to SRA <step3.rst>
        Confirm submission to SRA and fix errors <step4.rst>


Prerequisites

Note

To complete this tutorial, you must upload your FASTQ/SFF/BAM files to the CyVerse Data Store. See the Data Store Guide for instructions on how to upload your files (for example, using Cyberduck). Also, you will need detailed metadata about the sample being submitted ( e.g. collection/accession information, cell line/tissue metadata, etc.) and the sequencing platform used (e.g. library preparation strategy, sequencing instrument, etc.). These requirements will vary for the organism sequenced and are discussed in detail in the metadata section of this quickstart.

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise Register
NCBI Account Submissions will be sent to NCBI Register

Note

Register for an NCBI Account

If you do not have an NCBI account (you can check for an existing account logging in at https://www.ncbi.nlm.nih.gov/account/ ); register at https://www.ncbi.nlm.nih.gov/account/register/.

Platform(s)

We will use the following CyVerse platform(s):

Platform Interface Link Platform Documentation Quick Start
Data Store GUI/Command line Data Store Data Store Manual Guide
Discovery Environment Web/Point-and-click Discovery Environment DE Manual Guide

Input and example data

In order to complete this quickstart you will need to have the following inputs prepared

Input File(s) Format Preparation/Notes Example Data
FastQ/SFF/BAM files FastQ/SFF/BAM compressed (.gz/.bz2). For additional details see the SRA File Format Guide Sample truncated sample FastQ files

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